OpenRaiser/Intern-Atlas huggingface dataset:
Unsupervised Learning for Feature Extraction and Temporal Alignment of 3D+t Point Clouds of Zebrafish Embryos
Venue: arXiv cs.CV 2025
Year: 2025

Zebrafish are widely used in biomedical research and developmental stages of their embryos often need to be synchronized for further analysis. We present an unsupervised approach to extract descriptive features from 3D+t point clouds of zebrafish embryos and subsequently use those features to temporally align corresponding developmental stages. An autoencoder architecture is proposed to learn a descriptive representation of the point clouds and we designed a deep regression network for their temporal alignment. We achieve a high alignment accuracy with an average mismatch of only 3.83 minutes over an experimental duration of 5.3 hours. As a fully-unsupervised approach, there is no manual labeling effort required and unlike manual analyses the method easily scales. Besides, the alignment without human annotation of the data also avoids any influence caused by subjective bias.
Diffusion Models for Computational Neuroimaging: A Survey
Venue: arXiv cs.CV 2025
Year: 2025

Computational neuroimaging involves analyzing brain images or signals to provide mechanistic insights and predictive tools for human cognition and behavior. While diffusion models have shown stability and high-quality generation in natural images, there is increasing interest in adapting them to analyze brain data for various neurological tasks such as data enhancement, disease diagnosis and brain decoding. This survey provides an overview of recent efforts to integrate diffusion models into computational neuroimaging. We begin by introducing the common neuroimaging data modalities, follow with the diffusion formulations and conditioning mechanisms. Then we discuss how the variations of the denoising starting point, condition input and generation target of diffusion models are developed and enhance specific neuroimaging tasks. For a comprehensive overview of the ongoing research, we provide a publicly available repository at https://github.com/JoeZhao527/dm4neuro.
ProjectTest: A Project-level LLM Unit Test Generation Benchmark and Impact of Error Fixing Mechanisms
Venue: arXiv cs.SE 2025
Year: 2025

Unit test generation has become a promising and important use case of LLMs. However, existing evaluation benchmarks for assessing LLM unit test generation capabilities focus on function- or class-level code rather than more practical and challenging project-level codebases. To address such limitation, we propose ProjectTest, a project-level benchmark for unit test generation covering Python, Java, and JavaScript. ProjectTest features 20 moderate-sized and high-quality projects per language. We evaluate nine frontier LLMs on ProjectTest and the results show that all frontier LLMs tested exhibit moderate performance on ProjectTest on Python and Java, highlighting the difficulty of ProjectTest. We also conduct a thorough error analysis, which shows that even frontier LLMs, such as Claude-3.5-Sonnet, have significant basic yet critical errors, including compilation and cascade errors. Motivated by this observation, we further evaluate all frontier LLMs under manual error-fixing and self-error-fixing scenarios to assess their potential when equipped with error-fixing mechanisms. Our code and dataset is available at \href{https://github.com/YiboWANG214/ProjectTest}{ProjectTest}.
On the FirstFit Algorithm for Online Unit-Interval Coloring
Venue: arXiv cs.DS 2025
Year: 2025

In this paper, we study the performance of the FirstFit algorithm for the online unit-length intervals coloring problem where the intervals can be either open or closed, which serves a further investigation towards the actual performance of FirstFit. We develop a sophisticated counting method by generalizing the classic neighborhood bound, which limits the color FirstFit can assign an interval by counting the potential intersections. In the generalization, we show that for any interval, there is a critical interval intersecting it that can help reduce the overestimation of the number of intersections, and it further helps bound the color an interval can be assigned. The technical challenge then falls on identifying these critical intervals that guarantee the effectiveness of counting. Using this new mechanism for bounding the color that FirstFit can assign an interval, we provide a tight analysis of $2ω$ colors when all intervals have integral endpoints and an upper bound of $\lceil\frac{7}{3}ω\rceil-2$ colors for the general case, where $ω$ is the optimal number of colors needed for the input set of intervals.
The Minimal Search Space for Conditional Causal Bandits
Venue: arXiv cs.LG 2025
Year: 2025

Causal knowledge can be used to support decision-making problems. This has been recognized in the causal bandits literature, where a causal (multi-armed) bandit is characterized by a causal graphical model and a target variable. The arms are then interventions on the causal model, and rewards are samples of the target variable. Causal bandits were originally studied with a focus on hard interventions. We focus instead on cases where the arms are conditional interventions, which more accurately model many real-world decision-making problems by allowing the value of the intervened variable to be chosen based on the observed values of other variables. This paper presents a graphical characterization of the minimal set of nodes guaranteed to contain the optimal conditional intervention, which maximizes the expected reward. We then propose an efficient algorithm with a time complexity of $O(|V| + |E|)$ to identify this minimal set of nodes. We prove that the graphical characterization and the proposed algorithm are correct. Finally, we empirically demonstrate that our algorithm significantly prunes the search space and substantially accelerates convergence rates when integrated into standard multi-armed bandit algorithms.
Extract-QD Framework: A Generic Approach for Quality-Diversity in Noisy, Stochastic or Uncertain Domains
Venue: arXiv cs.NE 2025
Year: 2025

Quality-Diversity (QD) has demonstrated potential in discovering collections of diverse solutions to optimisation problems. Originally designed for deterministic environments, QD has been extended to noisy, stochastic, or uncertain domains through various Uncertain-QD (UQD) methods. However, the large number of UQD methods, each with unique constraints, makes selecting the most suitable one challenging. To remedy this situation, we present two contributions: first, the Extract-QD Framework (EQD Framework), and second, Extract-ME (EME), a new method derived from it. The EQD Framework unifies existing approaches within a modular view, and facilitates developing novel methods by interchanging modules. We use it to derive EME, a novel method that consistently outperforms or matches the best existing methods on standard benchmarks, while previous methods show varying performance. In a second experiment, we show how our EQD Framework can be used to augment existing QD algorithms and in particular the well-established Policy-Gradient-Assisted-MAP-Elites method, and demonstrate improved performance in uncertain domains at no additional evaluation cost. For any new uncertain task, our contributions now provide EME as a reliable "first guess" method, and the EQD Framework as a tool for developing task-specific approaches. Together, these contributions aim to lower the cost of adopting UQD insights in QD applications.
Diffeomorphic Temporal Alignment Nets for Time-series Joint Alignment and Averaging
Venue: arXiv cs.LG 2025
Year: 2025

In time-series analysis, nonlinear temporal misalignment remains a pivotal challenge that forestalls even simple averaging. Since its introduction, the Diffeomorphic Temporal Alignment Net (DTAN), which we first introduced (Weber et al., 2019) and further developed in (Weber & Freifeld, 2023), has proven itself as an effective solution for this problem (these conference papers are earlier partial versions of the current manuscript). DTAN predicts and applies diffeomorphic transformations in an input-dependent manner, thus facilitating the joint alignment (JA) and averaging of time-series ensembles in an unsupervised or a weakly-supervised manner. The inherent challenges of the weakly/unsupervised setting, particularly the risk of trivial solutions through excessive signal distortion, are mitigated using either one of two distinct strategies: 1) a regularization term for warps; 2) using the Inverse Consistency Averaging Error (ICAE). The latter is a novel, regularization-free approach which also facilitates the JA of variable-length signals. We also further extend our framework to incorporate multi-task learning (MT-DTAN), enabling simultaneous time-series alignment and classification. Additionally, we conduct a comprehensive evaluation of different backbone architectures, demonstrating their efficacy in time-series alignment tasks. Finally, we showcase the utility of our approach in enabling Principal Component Analysis (PCA) for misaligned time-series data. Extensive experiments across 128 UCR datasets validate the superiority of our approach over contemporary averaging methods, including both traditional and learning-based approaches, marking a significant advancement in the field of time-series analysis.
Amortized In-Context Bayesian Posterior Estimation
Venue: arXiv cs.LG 2025
Year: 2025

Bayesian inference provides a natural way of incorporating prior beliefs and assigning a probability measure to the space of hypotheses. Current solutions rely on iterative routines like Markov Chain Monte Carlo (MCMC) sampling and Variational Inference (VI), which need to be re-run whenever new observations are available. Amortization, through conditional estimation, is a viable strategy to alleviate such difficulties and has been the guiding principle behind simulation-based inference, neural processes and in-context methods using pre-trained models. In this work, we conduct a thorough comparative analysis of amortized in-context Bayesian posterior estimation methods from the lens of different optimization objectives and architectural choices. Such methods train an amortized estimator to perform posterior parameter inference by conditioning on a set of data examples passed as context to a sequence model such as a transformer. In contrast to language models, we leverage permutation invariant architectures as the true posterior is invariant to the ordering of context examples. Our empirical study includes generalization to out-of-distribution tasks, cases where the assumed underlying model is misspecified, and transfer from simulated to real problems. Subsequently, it highlights the superiority of the reverse KL estimator for predictive problems, especially when combined with the transformer architecture and normalizing flows.
A Frontier AI Risk Management Framework: Bridging the Gap Between Current AI Practices and Established Risk Management
Venue: arXiv cs.AI 2025
Year: 2025

The recent development of powerful AI systems has highlighted the need for robust risk management frameworks in the AI industry. Although companies have begun to implement safety frameworks, current approaches often lack the systematic rigor found in other high-risk industries. This paper presents a comprehensive risk management framework for the development of frontier AI that bridges this gap by integrating established risk management principles with emerging AI-specific practices. The framework consists of four key components: (1) risk identification (through literature review, open-ended red-teaming, and risk modeling), (2) risk analysis and evaluation using quantitative metrics and clearly defined thresholds, (3) risk treatment through mitigation measures such as containment, deployment controls, and assurance processes, and (4) risk governance establishing clear organizational structures and accountability. Drawing from best practices in mature industries such as aviation or nuclear power, while accounting for AI's unique challenges, this framework provides AI developers with actionable guidelines for implementing robust risk management. The paper details how each component should be implemented throughout the life-cycle of the AI system - from planning through deployment - and emphasizes the importance and feasibility of conducting risk management work prior to the final training run to minimize the burden associated with it.
No Trick, No Treat: Pursuits and Challenges Towards Simulation-free Training of Neural Samplers
Venue: arXiv cs.LG 2025
Year: 2025

We consider the sampling problem, where the aim is to draw samples from a distribution whose density is known only up to a normalization constant. Recent breakthroughs in generative modeling to approximate a high-dimensional data distribution have sparked significant interest in developing neural network-based methods for this challenging problem. However, neural samplers typically incur heavy computational overhead due to simulating trajectories during training. This motivates the pursuit of simulation-free training procedures of neural samplers. In this work, we propose an elegant modification to previous methods, which allows simulation-free training with the help of a time-dependent normalizing flow. However, it ultimately suffers from severe mode collapse. On closer inspection, we find that nearly all successful neural samplers rely on Langevin preconditioning to avoid mode collapsing. We systematically analyze several popular methods with various objective functions and demonstrate that, in the absence of Langevin preconditioning, most of them fail to adequately cover even a simple target. Finally, we draw attention to a strong baseline by combining the state-of-the-art MCMC method, Parallel Tempering (PT), with an additional generative model to shed light on future explorations of neural samplers.
Can 1B LLM Surpass 405B LLM? Rethinking Compute-Optimal Test-Time Scaling
Venue: arXiv cs.CL 2025
Year: 2025

Test-Time Scaling (TTS) is an important method for improving the performance of Large Language Models (LLMs) by using additional computation during the inference phase. However, current studies do not systematically analyze how policy models, Process Reward Models (PRMs), and problem difficulty influence TTS. This lack of analysis limits the understanding and practical use of TTS methods. In this paper, we focus on two core questions: (1) What is the optimal approach to scale test-time computation across different policy models, PRMs, and problem difficulty levels? (2) To what extent can extended computation improve the performance of LLMs on complex tasks, and can smaller language models outperform larger ones through this approach? Through comprehensive experiments on MATH-500 and challenging AIME24 tasks, we have the following observations: (1) The compute-optimal TTS strategy is highly dependent on the choice of policy model, PRM, and problem difficulty. (2) With our compute-optimal TTS strategy, extremely small policy models can outperform larger models. For example, a 1B LLM can exceed a 405B LLM on MATH-500. Moreover, on both MATH-500 and AIME24, a 0.5B LLM outperforms GPT-4o, a 3B LLM surpasses a 405B LLM, and a 7B LLM beats o1 and DeepSeek-R1, while with higher inference efficiency. These findings show the significance of adapting TTS strategies to the specific characteristics of each task and model and indicate that TTS is a promising approach for enhancing the reasoning abilities of LLMs.
RSAttAE: An Information-Aware Attention-based Autoencoder Recommender System
Venue: arXiv cs.LG 2025
Year: 2025

Recommender systems play a crucial role in modern life, including information retrieval, the pharmaceutical industry, retail, and entertainment. The entertainment sector, in particular, attracts significant attention and generates substantial profits. This work proposes a new method for predicting unknown user-movie ratings to enhance customer satisfaction. To achieve this, we utilize the MovieLens 100K dataset. Our approach introduces an attention-based autoencoder to create meaningful representations and the XGBoost method for rating predictions. The results demonstrate that our proposal outperforms most of the existing state-of-the-art methods. Availability: github.com/ComputationIASBS/RecommSys
Gradient Multi-Normalization for Stateless and Scalable LLM Training
Venue: arXiv cs.LG 2025
Year: 2025

Training large language models (LLMs) typically relies on adaptive optimizers like Adam (Kingma & Ba, 2015) which store additional state information to accelerate convergence but incur significant memory overhead. Recent efforts, such as SWAN (Ma et al., 2024) address this by eliminating the need for optimizer states while achieving performance comparable to Adam via a multi-step preprocessing procedure applied to instantaneous gradients. Motivated by the success of SWAN, we introduce a novel framework for designing stateless optimizers that normalizes stochastic gradients according to multiple norms. To achieve this, we propose a simple alternating scheme to enforce the normalization of gradients w.r.t these norms. We show that our procedure can produce, up to an arbitrary precision, a fixed-point of the problem, and that SWAN is a particular instance of our approach with carefully chosen norms, providing a deeper understanding of its design. However, SWAN's computationally expensive whitening/orthogonalization step limit its practicality for large LMs. Using our principled perspective, we develop of a more efficient, scalable, and practical stateless optimizer. Our algorithm relaxes the properties of SWAN, significantly reducing its computational cost while retaining its memory efficiency, making it applicable to training large-scale models. Experiments on pre-training LLaMA models with up to 1 billion parameters demonstrate a 3X speedup over Adam with significantly reduced memory requirements, outperforming other memory-efficient baselines.
Rationalization Models for Text-to-SQL
Venue: arXiv cs.CL 2025
Year: 2025

We introduce a framework for generating Chain-of-Thought (CoT) rationales to enhance text-to-SQL model fine-tuning. These rationales consist of intermediate SQL statements and explanations, serving as incremental steps toward constructing the final SQL query. The process begins with manually annotating a small set of examples, which are then used to prompt a large language model in an iterative, dynamic few-shot knowledge distillation procedure from a teacher model. A rationalization model is subsequently trained on the validated decomposed queries, enabling extensive synthetic CoT annotations for text-to-SQL datasets. To evaluate the approach, we fine-tune small language models with and without these rationales on the BIRD dataset. Results indicate that step-by-step query generation improves execution accuracy, especially for moderately and highly complex queries, while also enhancing explainability.
Lumina-Video: Efficient and Flexible Video Generation with Multi-scale Next-DiT
Venue: arXiv cs.CV 2025
Year: 2025

Recent advancements have established Diffusion Transformers (DiTs) as a dominant framework in generative modeling. Building on this success, Lumina-Next achieves exceptional performance in the generation of photorealistic images with Next-DiT. However, its potential for video generation remains largely untapped, with significant challenges in modeling the spatiotemporal complexity inherent to video data. To address this, we introduce Lumina-Video, a framework that leverages the strengths of Next-DiT while introducing tailored solutions for video synthesis. Lumina-Video incorporates a Multi-scale Next-DiT architecture, which jointly learns multiple patchifications to enhance both efficiency and flexibility. By incorporating the motion score as an explicit condition, Lumina-Video also enables direct control of generated videos' dynamic degree. Combined with a progressive training scheme with increasingly higher resolution and FPS, and a multi-source training scheme with mixed natural and synthetic data, Lumina-Video achieves remarkable aesthetic quality and motion smoothness at high training and inference efficiency. We additionally propose Lumina-V2A, a video-to-audio model based on Next-DiT, to create synchronized sounds for generated videos. Codes are released at https://www.github.com/Alpha-VLLM/Lumina-Video.
A Unified Knowledge-Distillation and Semi-Supervised Learning Framework to Improve Industrial Ads Delivery Systems
Venue: arXiv cs.LG 2025
Year: 2025

Industrial ads ranking systems conventionally rely on labeled impression data, which leads to challenges such as overfitting, slower incremental gain from model scaling, and biases due to discrepancies between training and serving data. To overcome these issues, we propose a Unified framework for Knowledge-Distillation and Semi-supervised Learning (UKDSL) for ads ranking, empowering the training of models on a significantly larger and more diverse datasets, thereby reducing overfitting and mitigating training-serving data discrepancies. We provide detailed formal analysis and numerical simulations on the inherent miscalibration and prediction bias of multi-stage ranking systems, and show empirical evidence of the proposed framework's capability to mitigate those. Compared to prior work, UKDSL can enable models to learn from a much larger set of unlabeled data, hence, improving the performance while being computationally efficient. Finally, we report the successful deployment of UKDSL in an industrial setting across various ranking models, serving users at multi-billion scale, across various surfaces, geological locations, clients, and optimize for various events, which to the best of our knowledge is the first of its kind in terms of the scale and efficiency at which it operates.
Exploring Model Invariance with Discrete Search for Ultra-Low-Bit Quantization
Venue: arXiv cs.LG 2025
Year: 2025

Large language models have been increasing in size due to their success in a wide range of applications. This calls for a pressing need to reduce memory usage to make them more accessible. Post-training quantization is a popular technique which uses fewer bits (e.g., 4--8 bits) to represent the model without retraining it. However, it remains a challenging task to perform quantization in an ultra-low-bit setup (e.g., 2 bits). In this paper, we propose InvarExplore, a unified framework that systematically explores different model invariance at the same time, allowing us to take advantage of the synergy between each type of invariance. Importantly, InvarExplore features a discrete search algorithm that enables us to explore permutation invariance, which is under-studied as it cannot be optimized with gradient-based methods. Results show that InvarExplore is compatible with existing state-of-the-art methods, achieving an add-on performance improvement over strong competing methods.